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Re: mdb fragmentation

Hi Geert,

If I could, I would delete 8664 from the ITS system entirely as it was filed based on invalid information that was provided to me.  It generally should be ignored.

When a write operation is performed with LMDB, the freelist is scanned for available space to reuse if possible.  The larger the size of the freelist, the longer amount of time it will take for the operation to complete successfully.  When the database has gotten to a certain point of fragmentation (This differs based on any individual use case), it will be start taking a noticeable amount of time for those write operations to complete and the server processing the write operation does essentially come to a halt during this process.  Once the write operation completes, things go back to normal.  The only solution is to dump and reload the database (slapcat/slapadd or mdb_copy -c). Eventually, you will get back into the same situation and have to do this again.

A recent option was added to the slapd-mdb configuration (rtxnsize) that can also help reduce the rate of fragmentation.  There are some performance related issues you can find discussed on the -devel list from when it was added.  Whether or not you are affected by them and whether or not the setting will help you in particular depends on whether or not your searches result in a large number of entries being returned.  You can find some guidelines around tuning the parameter that I came up with in that thread.  If you do not have an unlimited Zimbra License, the license check performed by the store servers will definitely affect this, since the result set is all active accounts which can be quite large.

Additionally, I had at one point had a patch for the Zimbra build of OpenLDAP that made it very aggressive in finding freespace to reuse.  I don't recall if it is still applied (I don't believe it currently is based on what I saw in github).  It basically meant that in Zimbra, it would work extra hard to find reusable freespace, which would reduce the rate at which the database would fragment, but it also meant that once the DB was fragmented enough, it would amplify the amount of time it took for a write op to complete.  I.e., it was a tradeoff of a longer time to reach a catastrophic state, but the state was more catastrophic once achieved.

This is one area where LMDB differs significantly from back-hdb/bdb.  You could have back-bdb/hdb databases that endured a high rate of write operations be in effect for years w/o needing maintenance.  With LMDB, you get better read & write rates, but it requires periodic reloads.

Hope this helps!


----- Original Message -----
> From: "Geert Hendrickx" <geert@hendrickx.be>
> To: "openldap-technical" <openldap-technical@openldap.org>
> Sent: Thursday, August 24, 2017 4:53:32 AM
> Subject: mdb fragmentation

> Hi
> We have an OpenLDAP 2.4.44 based, 4-way MMR setup with 4 M entries,
> which is fairly write intensive (Zimbra).
> Lately we've seen very frequent lockups of the master that receives
> the updates (only 1 out of 4), whereas the replicas stay responsive.
> According to -d stats logs, all threads suddenly take a long time to
> answer any queries, and slapd can no longer accept new connections.
> The issue always disappears again without intervention, but usually
> hits a number of times in a row, on an almost daily basis.
> We tested a lot of things, but eventually "solved" the issue with a
> slapcat and slapadd of the database - the master server has been
> completely stable again since.  The mdb was also reduced 50% in size.
> Looking at the old mdb (prior to the dump), mdb_stat -f shows it had
> over 3.7 M free pages.  Could it be an issue of database fragmentation
> similar to ITS#8664?
> Is it natural that the freelist (and thus the mdb) gets this big over
> time, I would expect those free pages to get reused constantly?
> And in that case would it make sense to monitor the number of free
> pages?  Is there a threshold to look for, before things get problematic
> again?  (ITS#7770 would come handy here, as we already monitor/graph
> various metrics from the monitor backend)
>	Geert
> --
> geert.hendrickx.be :: geert@hendrickx.be :: PGP: 0xC4BB9E9F
> This e-mail was composed using 100% recycled spam messages!


Quanah Gibson-Mount
Product Architect
Symas Corporation
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